git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6998 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/msi2lmp/README

@@ -1,3 +1,12 @@
+Stephanie Teich-McGoldrick (Sandai) is the current maintainer
+of the msi2lmp tool.  She can be contacted at steichm at sandia.gov
+
+23 Sep 2011
+
+added support for triclinic boxes
+see msi2lmp/TriclinicModification.pdf doc for details
+
+-----------------------------
 
  msi2lmp V3.6 4/10/2005
 

tools/msi2lmp/src/GetParameters.c

@@ -736,8 +736,8 @@ void GetParameters(int Forcefield)
 		    ooptypes[i].types[3]);
 
       ooptypes[i].angleangle_params[3] = tabc;
-      ooptypes[i].angleangle_params[4] = tabd;
+      ooptypes[i].angleangle_params[4] = tcbd;
-      ooptypes[i].angleangle_params[5] = tcbd;
+      ooptypes[i].angleangle_params[5] = tabd;
 
       k = find_angleangle_data(potential_types,ff_angang,kloc);
       if (k < 0) {

tools/msi2lmp/src/Makefile

@@ -18,7 +18,7 @@ OBJS     = $(SRCS:.c=.o)
 HEADERS  = Msi2LMP2.h Forcefield.h
 
 CC       = gcc
-CFLAGS   = -O2
+CFLAGS   = -O3
 FRCFILE  = cvff.frc
 FRCFILE2 = cff91.frc
 README   = README

tools/msi2lmp/src/Msi2LMP2.h

@@ -61,6 +61,8 @@
 #define MAX_CONNECTIONS 6
 #define MAX_STRING 50
 
+
+
 struct ResidueList {
   int start;
   int end;
@@ -168,6 +170,8 @@ _EX  char   rootname[20];
 _EX  char   path[20];
 _EX  double pbc[9];
 _EX  int    periodic   _ARG( 1 ); /* 0= nonperiodic 1= 3-D periodic */
+// Added triclinic flag for non-orthogonal boxes Oct 5, 2010 SLTM
+_EX  int TriclinicFlag; // 1 for non-orthoganal boxes, 0 for orthogonal boxes
 _EX  int    forcefield _ARG( 0 ); /* 0= ClassI      1= ClassII */
 _EX  int    pflag;
 _EX  int    *no_atoms;

tools/msi2lmp/src/ReadCarFile.c

@@ -12,6 +12,13 @@ void ReadCarFile(void)
    int skip;			/* lines to skip at beginning of file */
    double  lowest, highest;	/* temp coordinate finding variables */
    double total_q;
+   double sq_c;
+	double cos_alpha;  // Added by SLTM Sept 13, 2010
+	double cos_gamma;
+	double sin_gamma;
+	double cos_beta;
+	double sin_beta;
+    double A, B, C;
 
 /* Open .car file for reading */
 
@@ -39,10 +46,12 @@ void ReadCarFile(void)
      fgets(line,MAX_LINE_LENGTH,CarF); /* Date stamp */
       fscanf(CarF,"%*s %lf %lf %lf %lf %lf %lf %*s",
 	     &pbc[0],&pbc[1],&pbc[2],&pbc[3],&pbc[4],&pbc[5]);
+      
+	  // Added triclinic flag for non-orthogonal boxes Oct 5, 2010 SLTM 
 	  if(pbc[3] != 90.0 || pbc[4] != 90.0 || pbc[5] != 90.0) {
-         fprintf(stderr,"The system is not rectangular- LAMMPS can't handle it!!");
+         TriclinicFlag = 1;
-         exit(2);
       }
+      else TriclinicFlag = 0;
    }
    else {
       periodic = 0;
@@ -142,6 +151,9 @@ void ReadCarFile(void)
 /* Search coordinates to find lowest and highest for x, y, and z */
 
    if (periodic == 0) {
+    // Added if/else statment STLM Oct 5 2010
+    if (TriclinicFlag == 0)
+    {
        for ( k = 0; k < 3; k++) {
            lowest  = atoms[0].x[k];
            highest = atoms[0].x[k];
@@ -155,11 +167,44 @@ void ReadCarFile(void)
        }
     }
     else {
+        printf("Code only works for periodic systems with triclinic boxes");
+        exit(2);
+    }
+
+   }
+   else {
+       // Modified lines 176 - 201 Oct 5th 2010
+       if (TriclinicFlag == 0) {
            for (k=0; k < 3; k++) {
                  pbc[k+3] = pbc[k];
                  pbc[k] = 0.0;
            }
        }
+       else {
+           sq_c = pbc[2]*pbc[2];
+           cos_alpha = cos(pbc[3]*3.14159265358979323846/180.0);
+           cos_gamma = cos(pbc[5]*3.14159265358979323846/180.0);
+           sin_gamma = sin(pbc[5]*3.14159265358979323846/180.0);
+           cos_beta =  cos(pbc[4]*3.14159265358979323846/180.0);
+           sin_beta =  sin(pbc[4]*3.14159265358979323846/180.0);
+           printf("pbc[3] %lf pbc[4] %lf pbc[5] %lf\n", pbc[3] ,pbc[4] ,pbc[5]);
+           printf("cos_alpha %lf cos_beta %lf cos_gamma %lf\n", cos_alpha ,cos_beta ,cos_gamma);
+           A = pbc[0];
+           B = pbc[1];
+           C = pbc[2];
+           
+           
+           pbc[0] = A;
+           pbc[1] = B*sin_gamma;
+           pbc[2] = sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma);
+           pbc[3] = B * cos_gamma; // This is xy SLTM
+           pbc[4] = C * cos_beta; // This is xz SLTM
+           pbc[5] = C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma; // This is yz SLTM
+       }
+
+        
+      
+   }
 
 /* Close .car file */
    

tools/msi2lmp/src/WriteDataFile.c

@@ -38,10 +38,13 @@ void WriteDataFile(FILE *DatF,char *nameroot,int forcefield)
        fprintf  (DatF, " %3d improper types\n", no_oop_types);
    }
    
+   
    fprintf(DatF, "\n");
-   fprintf(DatF, " %15.9f %15.9f xlo xhi\n", pbc[0], pbc[3]);
+   fprintf(DatF, " %15.9f %15.9f xlo xhi\n", 0.0, pbc[0]);
-   fprintf(DatF, " %15.9f %15.9f ylo yhi\n", pbc[1], pbc[4]);
+   fprintf(DatF, " %15.9f %15.9f ylo yhi\n", 0.0, pbc[1]);
-   fprintf(DatF, " %15.9f %15.9f zlo zhi\n", pbc[2], pbc[5]);
+   fprintf(DatF, " %15.9f %15.9f zlo zhi\n", 0.0, pbc[2]);
+   fprintf(DatF, " %15.9f %15.9f %15.9f xy xz yz\n", pbc[3], pbc[4], pbc[5]);
+   
 
    /* MASSES */
 

tools/msi2lmp/src/WriteDataFile05.c

@@ -50,10 +50,23 @@ void WriteDataFile05(char *nameroot,int forcefield)
        fprintf  (DatF, " %3d improper types\n", no_oop_types);
    }
 	
+	
+	// Modified by SLTM to print out triclinic box types 10/05/10 - lines 56-68
+   
+    if (TriclinicFlag == 0) {
         fprintf(DatF, "\n");
         fprintf(DatF, " %15.9f %15.9f xlo xhi\n", pbc[0], pbc[3]);
         fprintf(DatF, " %15.9f %15.9f ylo yhi\n", pbc[1], pbc[4]);
         fprintf(DatF, " %15.9f %15.9f zlo zhi\n", pbc[2], pbc[5]);
+    }
+    else {
+        fprintf(DatF, "\n");
+        fprintf(DatF, " %15.9f %15.9f xlo xhi\n", 0.0, pbc[0]);
+        fprintf(DatF, " %15.9f %15.9f ylo yhi\n", 0.0, pbc[1]);
+        fprintf(DatF, " %15.9f %15.9f zlo zhi\n", 0.0, pbc[2]);
+        fprintf(DatF, " %15.9f %15.9f %15.9f xy xz yz\n", pbc[3], pbc[4], pbc[5]);	
+    }
+	
 	
    /* MASSES */
 
@@ -113,7 +126,10 @@ void WriteDataFile05(char *nameroot,int forcefield)
      for (i=0; i < no_dihedral_types; i++) {
        fprintf(DatF, "%3i ", i+1);
        for ( j = 0; j < m; j++)
+           // Modified on 10/05/2010 by STLM to match with lammps reading in integers for the all but the first coefficients
+           if (j == 0)
                fprintf(DatF, "%10.4f ", dihedraltypes[i].params[j]);
+           else fprintf(DatF, "%10.0f ", dihedraltypes[i].params[j]);
        fprintf(DatF,"\n");
      }
      fprintf(DatF, "\n");
@@ -124,7 +140,10 @@ void WriteDataFile05(char *nameroot,int forcefield)
        for (i=0; i < no_oop_types; i++) {
 	 fprintf(DatF, "%3i ", i+1);
 	 for ( j = 0; j < 3; j++)
+         // Modified on 10/05/2010 by STLM to match with lammps reading in integers for the all but the first coefficients
+         if (j == 0)
              fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+         else fprintf(DatF, "%10.0f ", ooptypes[i].params[j]);
 	 fprintf(DatF, "\n");
        }
        fprintf(DatF, "\n");

tools/msi2lmp/src/msi2lmp.c

@@ -142,7 +142,7 @@ int main (int argc, char *argv[])
    frc_dir_name = getenv("BIOSYM_LIBRARY");
     
    if (frc_dir_name == NULL) {
-     frc_file_name = strcpy(frc_file_name,"./cvff.frc");
+    frc_file_name = strcpy(frc_file_name,"../biosym_frc_files/clayff.frc");
    }
    else {
      for (i=0; i < strlen(frc_dir_name); i++)
@@ -150,6 +150,8 @@ int main (int argc, char *argv[])
      frc_file_name = strcat(frc_file_name,"/cvff.frc");
    }
 
+    
+    
    if (argc < 2) { /* If no rootname was supplied, prompt for it */
      fprintf(stderr,"The rootname of the .car and .mdf files must be entered\n");
    }
@@ -223,13 +225,13 @@ int main (int argc, char *argv[])
    }
 
  /* Read in .car file */
-
+    printf("I am before read car file\n");
    ReadCarFile();
-
+   printf("I am after read car file\n");
  /*Read in .mdf file */
 
    ReadMdfFile();
-
+   printf("I am after read mdf file\n");
  /* Define bonds, angles, etc...*/
 
    if (pflag > 0) fprintf(stderr,"\n Building internal coordinate lists \n");
@@ -237,6 +239,7 @@ int main (int argc, char *argv[])
 
  /* Read .frc file into memory */
 	
+  // Commented out to create conversion file suitable for non-orthogonal boxes Sept 13, 2010 SLTM  	
    if (pflag > 0) fprintf(stderr,"\n Reading forcefield file \n");
    ReadFrcFile();